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load dataset
ctrl_filtered <- readRDS("./processed_data_file/ctrl_filtered.rds")
HSD_filtered <- readRDS("./processed_data_file/HSD_filtered.rds")
umapplot(ctrl_filtered, group.by = "ref_celltype")
Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

umapplot(HSD_filtered, group.by = "ref_celltype")
Scale for 'colour' is already present. Adding another scale for 'colour', which will
replace the existing scale.

scmap
ref_sce <- mkref_scmap_from_seuobj(ctrl_filtered)
Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)
HSD_filtered <- query_scmap_from_refsce(HSD_filtered, ref_sce, ref_labels = 'celltype')
Parameter M was not provided, will use M = n_features / 10 (if n_features <= 1000), where n_features is the number of selected features, and M = 100 otherwise.
Parameter k was not provided, will use k = sqrt(number_of_cells)
umapplot(HSD_filtered,group.by = "scmap_idents")
Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the
existing scale.

prop_confuse_mat
ASP DB DT SB PC TC VB
ASP 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
DB 0.0000000000 0.9623103279 0.0110732538 0.0000000000 0.0320699708 0.0000000000 0.0163487738
DT 0.0000000000 0.0063631914 0.9514480409 0.0064516129 0.0029154519 0.0000000000 0.0000000000
SB 0.0000000000 0.0004894763 0.0144804089 0.9935483871 0.0029154519 0.0370370370 0.0000000000
PC 0.0000000000 0.0181106216 0.0000000000 0.0000000000 0.9620991254 0.0000000000 0.0000000000
TC 0.0000000000 0.0000000000 0.0212947189 0.0000000000 0.0000000000 0.9629629630 0.0000000000
VB 0.0000000000 0.0073421439 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.9700272480
LT 0.0000000000 0.0053842389 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0136239782
GB 0.0000000000 0.0000000000 0.0008517888 0.0000000000 0.0000000000 0.0000000000 0.0000000000
LT GB
ASP 0.0000000000 0.0000000000
DB 0.0000000000 0.0000000000
DT 0.0092592593 0.0000000000
SB 0.0000000000 0.0000000000
PC 0.0000000000 0.0000000000
TC 0.0000000000 0.0000000000
VB 0.0000000000 0.0000000000
LT 0.9907407407 0.0000000000
GB 0.0000000000 1.0000000000
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